Job ID = 1293204 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 31,509,090 reads read : 31,509,090 reads written : 31,509,090 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: No such file or directory fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:08:15 31509090 reads; of these: 31509090 (100.00%) were unpaired; of these: 2632525 (8.35%) aligned 0 times 23988569 (76.13%) aligned exactly 1 time 4887996 (15.51%) aligned >1 times 91.65% overall alignment rate Time searching: 00:08:15 Overall time: 00:08:15 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 4404208 / 28876565 = 0.1525 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Sun, 02 Jun 2019 22:44:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402756/SRX5402756.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402756/SRX5402756.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402756/SRX5402756.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402756/SRX5402756.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sun, 02 Jun 2019 22:44:45: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:44:45: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:44:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402756/SRX5402756.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402756/SRX5402756.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402756/SRX5402756.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402756/SRX5402756.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sun, 02 Jun 2019 22:44:45: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:44:45: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:44:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402756/SRX5402756.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402756/SRX5402756.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402756/SRX5402756.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402756/SRX5402756.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sun, 02 Jun 2019 22:44:46: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:44:46: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:44:54: 1000000 INFO @ Sun, 02 Jun 2019 22:44:54: 1000000 INFO @ Sun, 02 Jun 2019 22:44:55: 1000000 INFO @ Sun, 02 Jun 2019 22:45:03: 2000000 INFO @ Sun, 02 Jun 2019 22:45:03: 2000000 INFO @ Sun, 02 Jun 2019 22:45:03: 2000000 INFO @ Sun, 02 Jun 2019 22:45:11: 3000000 INFO @ Sun, 02 Jun 2019 22:45:11: 3000000 INFO @ Sun, 02 Jun 2019 22:45:11: 3000000 INFO @ Sun, 02 Jun 2019 22:45:19: 4000000 INFO @ Sun, 02 Jun 2019 22:45:20: 4000000 INFO @ Sun, 02 Jun 2019 22:45:20: 4000000 INFO @ Sun, 02 Jun 2019 22:45:27: 5000000 INFO @ Sun, 02 Jun 2019 22:45:29: 5000000 INFO @ Sun, 02 Jun 2019 22:45:29: 5000000 INFO @ Sun, 02 Jun 2019 22:45:35: 6000000 INFO @ Sun, 02 Jun 2019 22:45:37: 6000000 INFO @ Sun, 02 Jun 2019 22:45:37: 6000000 INFO @ Sun, 02 Jun 2019 22:45:42: 7000000 INFO @ Sun, 02 Jun 2019 22:45:45: 7000000 INFO @ Sun, 02 Jun 2019 22:45:45: 7000000 INFO @ Sun, 02 Jun 2019 22:45:50: 8000000 INFO @ Sun, 02 Jun 2019 22:45:54: 8000000 INFO @ Sun, 02 Jun 2019 22:45:54: 8000000 INFO @ Sun, 02 Jun 2019 22:45:59: 9000000 INFO @ Sun, 02 Jun 2019 22:46:02: 9000000 INFO @ Sun, 02 Jun 2019 22:46:02: 9000000 INFO @ Sun, 02 Jun 2019 22:46:06: 10000000 INFO @ Sun, 02 Jun 2019 22:46:10: 10000000 INFO @ Sun, 02 Jun 2019 22:46:11: 10000000 INFO @ Sun, 02 Jun 2019 22:46:14: 11000000 INFO @ Sun, 02 Jun 2019 22:46:19: 11000000 INFO @ Sun, 02 Jun 2019 22:46:19: 11000000 INFO @ Sun, 02 Jun 2019 22:46:21: 12000000 INFO @ Sun, 02 Jun 2019 22:46:28: 12000000 INFO @ Sun, 02 Jun 2019 22:46:28: 12000000 INFO @ Sun, 02 Jun 2019 22:46:29: 13000000 INFO @ Sun, 02 Jun 2019 22:46:36: 13000000 INFO @ Sun, 02 Jun 2019 22:46:36: 13000000 INFO @ Sun, 02 Jun 2019 22:46:36: 14000000 INFO @ Sun, 02 Jun 2019 22:46:44: 15000000 INFO @ Sun, 02 Jun 2019 22:46:44: 14000000 INFO @ Sun, 02 Jun 2019 22:46:44: 14000000 INFO @ Sun, 02 Jun 2019 22:46:51: 16000000 INFO @ Sun, 02 Jun 2019 22:46:52: 15000000 INFO @ Sun, 02 Jun 2019 22:46:53: 15000000 INFO @ Sun, 02 Jun 2019 22:46:59: 17000000 INFO @ Sun, 02 Jun 2019 22:47:01: 16000000 INFO @ Sun, 02 Jun 2019 22:47:01: 16000000 INFO @ Sun, 02 Jun 2019 22:47:07: 18000000 INFO @ Sun, 02 Jun 2019 22:47:09: 17000000 INFO @ Sun, 02 Jun 2019 22:47:09: 17000000 INFO @ Sun, 02 Jun 2019 22:47:15: 19000000 INFO @ Sun, 02 Jun 2019 22:47:17: 18000000 INFO @ Sun, 02 Jun 2019 22:47:18: 18000000 INFO @ Sun, 02 Jun 2019 22:47:22: 20000000 INFO @ Sun, 02 Jun 2019 22:47:26: 19000000 INFO @ Sun, 02 Jun 2019 22:47:26: 19000000 INFO @ Sun, 02 Jun 2019 22:47:30: 21000000 INFO @ Sun, 02 Jun 2019 22:47:34: 20000000 INFO @ Sun, 02 Jun 2019 22:47:35: 20000000 INFO @ Sun, 02 Jun 2019 22:47:37: 22000000 INFO @ Sun, 02 Jun 2019 22:47:43: 21000000 INFO @ Sun, 02 Jun 2019 22:47:43: 21000000 INFO @ Sun, 02 Jun 2019 22:47:44: 23000000 INFO @ Sun, 02 Jun 2019 22:47:51: 22000000 INFO @ Sun, 02 Jun 2019 22:47:51: 22000000 INFO @ Sun, 02 Jun 2019 22:47:52: 24000000 INFO @ Sun, 02 Jun 2019 22:47:55: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:47:55: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:47:55: #1 total tags in treatment: 24472357 INFO @ Sun, 02 Jun 2019 22:47:55: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:47:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 22:47:56: #1 tags after filtering in treatment: 24472357 INFO @ Sun, 02 Jun 2019 22:47:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:47:56: #1 finished! INFO @ Sun, 02 Jun 2019 22:47:56: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:47:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:47:59: #2 number of paired peaks: 122 WARNING @ Sun, 02 Jun 2019 22:47:59: Fewer paired peaks (122) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 122 pairs to build model! INFO @ Sun, 02 Jun 2019 22:47:59: start model_add_line... INFO @ Sun, 02 Jun 2019 22:47:59: start X-correlation... INFO @ Sun, 02 Jun 2019 22:47:59: end of X-cor INFO @ Sun, 02 Jun 2019 22:47:59: #2 finished! INFO @ Sun, 02 Jun 2019 22:47:59: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 22:47:59: #2 alternative fragment length(s) may be 1,43,117,460,484,563,576 bps INFO @ Sun, 02 Jun 2019 22:47:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402756/SRX5402756.10_model.r WARNING @ Sun, 02 Jun 2019 22:47:59: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 22:47:59: #2 You may need to consider one of the other alternative d(s): 1,43,117,460,484,563,576 WARNING @ Sun, 02 Jun 2019 22:47:59: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 22:47:59: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:47:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:47:59: 23000000 INFO @ Sun, 02 Jun 2019 22:48:00: 23000000 INFO @ Sun, 02 Jun 2019 22:48:08: 24000000 INFO @ Sun, 02 Jun 2019 22:48:08: 24000000 INFO @ Sun, 02 Jun 2019 22:48:12: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:48:12: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:48:12: #1 total tags in treatment: 24472357 INFO @ Sun, 02 Jun 2019 22:48:12: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:48:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 22:48:12: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:48:12: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:48:12: #1 total tags in treatment: 24472357 INFO @ Sun, 02 Jun 2019 22:48:12: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:48:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 22:48:13: #1 tags after filtering in treatment: 24472357 INFO @ Sun, 02 Jun 2019 22:48:13: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:48:13: #1 finished! INFO @ Sun, 02 Jun 2019 22:48:13: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:48:13: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:48:13: #1 tags after filtering in treatment: 24472357 INFO @ Sun, 02 Jun 2019 22:48:13: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:48:13: #1 finished! INFO @ Sun, 02 Jun 2019 22:48:13: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:48:13: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:48:15: #2 number of paired peaks: 122 WARNING @ Sun, 02 Jun 2019 22:48:15: Fewer paired peaks (122) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 122 pairs to build model! INFO @ Sun, 02 Jun 2019 22:48:15: start model_add_line... INFO @ Sun, 02 Jun 2019 22:48:16: start X-correlation... INFO @ Sun, 02 Jun 2019 22:48:16: #2 number of paired peaks: 122 WARNING @ Sun, 02 Jun 2019 22:48:16: Fewer paired peaks (122) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 122 pairs to build model! INFO @ Sun, 02 Jun 2019 22:48:16: start model_add_line... INFO @ Sun, 02 Jun 2019 22:48:16: end of X-cor INFO @ Sun, 02 Jun 2019 22:48:16: #2 finished! INFO @ Sun, 02 Jun 2019 22:48:16: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 22:48:16: #2 alternative fragment length(s) may be 1,43,117,460,484,563,576 bps INFO @ Sun, 02 Jun 2019 22:48:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402756/SRX5402756.20_model.r WARNING @ Sun, 02 Jun 2019 22:48:16: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 22:48:16: #2 You may need to consider one of the other alternative d(s): 1,43,117,460,484,563,576 WARNING @ Sun, 02 Jun 2019 22:48:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 22:48:16: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:48:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:48:16: start X-correlation... INFO @ Sun, 02 Jun 2019 22:48:16: end of X-cor INFO @ Sun, 02 Jun 2019 22:48:16: #2 finished! INFO @ Sun, 02 Jun 2019 22:48:16: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 22:48:16: #2 alternative fragment length(s) may be 1,43,117,460,484,563,576 bps INFO @ Sun, 02 Jun 2019 22:48:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402756/SRX5402756.05_model.r WARNING @ Sun, 02 Jun 2019 22:48:16: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 22:48:16: #2 You may need to consider one of the other alternative d(s): 1,43,117,460,484,563,576 WARNING @ Sun, 02 Jun 2019 22:48:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 22:48:16: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:48:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:48:53: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:49:09: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:49:09: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:49:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402756/SRX5402756.10_peaks.xls INFO @ Sun, 02 Jun 2019 22:49:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402756/SRX5402756.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:49:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402756/SRX5402756.10_summits.bed INFO @ Sun, 02 Jun 2019 22:49:17: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:49:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402756/SRX5402756.20_peaks.xls INFO @ Sun, 02 Jun 2019 22:49:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402756/SRX5402756.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:49:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402756/SRX5402756.20_summits.bed INFO @ Sun, 02 Jun 2019 22:49:33: Done! INFO @ Sun, 02 Jun 2019 22:49:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402756/SRX5402756.05_peaks.xls INFO @ Sun, 02 Jun 2019 22:49:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402756/SRX5402756.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:49:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402756/SRX5402756.05_summits.bed INFO @ Sun, 02 Jun 2019 22:49:33: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。